6H24 | pdb_00006h24

X-Ray Crystal Structure of the MSBI1.176 WH1 Domain, a Replication Protein Isolated from a Multiple Sclerosis Patient

• PDB DOI: https://doi.org/10.2210/pdb6H24/pdb

• Classification: REPLICATION
• Organism(s): Sphinx1.76-related DNA
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-07-13 Released: 2019-05-15 
• Deposition Author(s): Kilic, T., Popov, A.N., Hansman, G.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Structural analysis of a replication protein encoded by a plasmid isolated from a multiple sclerosis patient.

Kilic, T., Popov, A.N., Burk-Korner, A., Koromyslova, A., Zur Hausen, H., Bund, T., Hansman, G.S.

(2019) Acta Crystallogr D Struct Biol 75: 498-504

• PubMed: 31063152 
• DOI: https://doi.org/10.1107/S2059798319003991
• Primary Citation Related Structures: 
  6H24


• PubMed Abstract: 
  

  Bovine meat and milk factors (BMMFs) are circular, single-stranded episomal DNAs that have been detected in bovine meat and milk products. BMMFs are thought to have roles in human malignant and degenerative diseases. BMMFs encode a replication initiator protein (Rep) that is actively transcribed and translated in human cells. In this study, a Rep WH1 domain encoded on a BMMF (MSBI1.176) isolated from a multiple sclerosis human brain sample was determined to 1.53 Å resolution using X-ray crystallography. The overall structure of the MSBI1.176 WH1 domain was remarkably similar to other Rep structures, despite having a low (28%) amino-acid sequence identity. The MSBI1.176 WH1 domain contained elements common to other Reps, including five α-helices, five β-strands and a hydrophobic pocket. These new findings suggest that the MSBI1.176 Rep might have comparable roles and functions to other known Reps of different origins.

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Organizational Affiliation: 
• Schaller Research Group at the University of Heidelberg, Heidelberg, Germany.
Structural Biology Group, European Synchrotron Radiation Facility (ESRF), Grenoble, France.
German Cancer Research Center (DKFZ), Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.91 kDa 
• Atom Count: 2,180 
• Modeled Residue Count: 260 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replication protein	A, B	135	Sphinx1.76-related DNA	Mutation(s): 0  Gene Names: Rep
UniProt
Find proteins for A0A1T4J289 (Sphinx1.76-related DNA) Explore A0A1T4J289  Go to UniProtKB:  A0A1T4J289

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.38	α = 90
b = 77.77	β = 90.66
c = 47.68	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
HKL2Map	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Kilic, T., Popov, A.N., Hansman, G.S.

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references